In general, a mass spectrometer comprises an ion source for generating ions from molecules to be analysed, and ion optics for guiding the ions to a mass analyser. A tandem mass spectrometer further comprises a second mass analyser. In tandem mass spectrometry, structural elucidation of ionised molecules is performed by using the first mass analyser to collect a mass spectrum, then using the first mass analyser to select a desired precursor ion or ions from the mass spectrum, ejecting the chosen precursor ion(s) to a reaction cell where they are fragmented, and transporting the ions, including the fragmented ions, to the second mass analyser for collection of a mass spectrum of the fragment ions. The method can be extended to provide one or more further stages of fragmentation (i.e. fragmentation of fragment ions and so on). This is typically referred to as MSn, with n denoting the number of generations of ions. Thus MS2 corresponds to tandem mass spectrometry.
Tandem mass spectrometers can be classified into three types:
(1) sequential in space, corresponding to combinations of transmitting mass analysers (e.g. magnetic sectors, quadrupole, time-of-flight (TOF), usually with a collision cell in-between);
(2) sequential in time, corresponding to stand-alone trapping mass analysers (e.g. quadrupole, linear, Fourier transform ion cyclotron resonance (FT-ICR), electrostatic traps); and
(3) sequential in time and space, corresponding to hybrids of traps and transmitting mass analysers.
Most tandem mass spectrometers have different stages of mass analysis following each other along a common axis. Such “consecutive” geometry allows installation of an RF collision cell or an additional trapping stage, but precludes other apparatus such as:                an additional ion source (e.g. for introducing calibrant ions or ions of an opposite polarity);        a window for introducing laser radiation;        a surface for soft landing of ions (as described in WO03/105183);        a surface for surface-induced dissociation (SID); or        an electron source (e.g. for introducing electrons to effect electron capture dissociation (ECD), see WO02/078048 and WO03/102545).        
An example of a tandem mass spectrometer having consecutive geometry is provided by WO02/48699. This spectrometer comprises an ion source, a series of ion traps, one of which is operated as a collision cell, followed by a TOF analyser. Tandem mass analysis and MSn is performed by using multiple reversal of ion movement. This is effected by trapping ions, releasing them in the reverse direction, fragmenting, trapping of fragments, and repeating the cycle to generate the required number of ion generations. However, finally the fragments must pass back through all the ion traps to make their way to the consecutively-arranged TOF analyser.
A tandem mass spectrometer with a consecutive, although unusual, geometry is described in WO97/48120. An ion source generates ions that are accelerated orthogonally into a TOF analyser. The ions are reflected by an ion mirror: some of the ions are collected by the TOF detector, whereas some continue to a reaction cell placed after the TOF analyser where they may be fragmented. The fragmented ions are reflected to return along the reverse path into the TOF analyser to be collected by the TOF detector. The reaction cell may fragment the ions in one of three ways: collision induced dissociation (CID), SID or photon induced dissociation (PID). Although this geometry offers greater flexibility in the design and operation of the reaction cell, its utility is limited because of high ion losses caused by the low duty cycle of orthogonal pulsing.